Merge pull request #1179 from allenbaron/query_update

Exclude some synonym types from duplicate_exact_synonym report query

CHANGELOG.md

@@ -10,6 +10,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Added option to input template strings from external file [#1152]
 
+### Changed
+- Updated `duplicate_exact_syonym` [`report`] query to be case-insensitive and ignore synoyms annotated as abbreviation or acronym synonym types [#1179]
+
 ### Fixed
 - '--annotate-with-source true' does not work with extract --method subset [#1160]
 - Fix how Template adds entities to the QuotedEntityChecker [#1104]
@@ -388,6 +391,7 @@ First official release of ROBOT!
 [`validate`]: http://robot.obolibrary.org/validate
 ;
 [#1181]: https://github.com/ontodev/robot/pull/1181
+[#1179]: https://github.com/ontodev/robot/pull/1179
 [#1171]: https://github.com/ontodev/robot/pull/1171
 [#1168]: https://github.com/ontodev/robot/pull/1168
 [#1160]: https://github.com/ontodev/robot/pull/1160

docs/report_queries/duplicate_exact_synonym.md

@@ -1,27 +1,40 @@
 # Duplicate Exact Synonym
 
-**Problem:** Two entities share an exact synonym. This causes ambiguity. Excludes deprecated entities.
+**Problem:** Two entities share an exact synonym (case-insensitive). This causes ambiguity. Excludes deprecated entities and synonyms annotated as abbreviation or acronym.
 
-**Solution:** Avoid ambiguity by assigning unique exact synonyms or changing the exact synonym to a different annotation (e.g. broad synonym).
+**Solution:** Avoid ambiguity by assigning unique exact synonyms, changing the exact synonym to a different annotation (e.g. broad synonym), or annotating it as an abbreviation or acronym.
 
 ```sparql
 PREFIX obo: <http://purl.obolibrary.org/obo/>
 PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT DISTINCT ?entity ?property ?value WHERE {
-  VALUES ?property {
-    obo:IAO_0000118
-    oboInOwl:hasExactSynonym
+SELECT DISTINCT ?entity ?property ?value
+WHERE {
+  {
+    SELECT DISTINCT ?syn_std ?property (COUNT(DISTINCT ?entity) AS ?cnt)
+    WHERE {
+      VALUES ?property { obo:IAO_0000118 oboInOwl:hasExactSynonym }
+      ?entity ?property ?syn .
+      OPTIONAL {
+        VALUES ?syn_type { obo:OMO_0003000 obo:OMO_0003012 }
+        ?exclude a owl:Axiom ;
+              owl:annotatedSource ?entity ;
+              owl:annotatedProperty ?property ;
+              owl:annotatedTarget ?syn ;
+              oboInOwl:hasSynonymType ?syn_type .
+      }
+
+      BIND(UCASE(?syn) AS ?syn_std)
+      FILTER (!isBlank(?entity) && !BOUND(?exclude))
+      FILTER NOT EXISTS { ?entity owl:deprecated true }
+    } GROUP BY ?syn_std ?property HAVING (?cnt > 1)
   }
-  ?entity ?property ?value.
-  ?entity2 ?property ?value .
-  FILTER NOT EXISTS { ?entity owl:deprecated true }
-  FILTER NOT EXISTS { ?entity2 owl:deprecated true }
-  FILTER (?entity != ?entity2)
+  ?entity ?property ?value .
   FILTER (!isBlank(?entity))
-  FILTER (!isBlank(?entity2))
+  FILTER NOT EXISTS { ?entity owl:deprecated true }
+  FILTER (UCASE(?value) = ?syn_std)
 }
 ORDER BY DESC(UCASE(str(?value)))
-```
+```

robot-core/src/main/resources/report_queries/duplicate_exact_synonym.rq

@@ -1,25 +1,38 @@
 # # Duplicate Exact Synonym
 #
-# **Problem:** Two entities share an exact synonym. This causes ambiguity. Excludes deprecated entities.
+# **Problem:** Two entities share an exact synonym (case-insensitive). This causes ambiguity. Excludes deprecated entities and synonyms annotated as abbreviation or acronym.
 #
-# **Solution:** Avoid ambiguity by assigning unique exact synonyms or changing the exact synonym to a different annotation (e.g. broad synonym).
+# **Solution:** Avoid ambiguity by assigning unique exact synonyms, changing the exact synonym to a different annotation (e.g. broad synonym), or annotating it as an abbreviation or acronym.
 
 PREFIX obo: <http://purl.obolibrary.org/obo/>
 PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT DISTINCT ?entity ?property ?value WHERE {
-  VALUES ?property {
-    obo:IAO_0000118
-    oboInOwl:hasExactSynonym
+SELECT DISTINCT ?entity ?property ?value
+WHERE {
+  {
+    SELECT DISTINCT ?syn_std ?property (COUNT(DISTINCT ?entity) AS ?cnt)
+    WHERE {
+      VALUES ?property { obo:IAO_0000118 oboInOwl:hasExactSynonym }
+      ?entity ?property ?syn .
+      OPTIONAL {
+        VALUES ?syn_type { obo:OMO_0003000 obo:OMO_0003012 }
+        ?exclude a owl:Axiom ;
+              owl:annotatedSource ?entity ;
+              owl:annotatedProperty ?property ;
+              owl:annotatedTarget ?syn ;
+              oboInOwl:hasSynonymType ?syn_type .
+      }
+
+      BIND(UCASE(?syn) AS ?syn_std)
+      FILTER (!isBlank(?entity) && !BOUND(?exclude))
+      FILTER NOT EXISTS { ?entity owl:deprecated true }
+    } GROUP BY ?syn_std ?property HAVING (?cnt > 1)
   }
-  ?entity ?property ?value.
-  ?entity2 ?property ?value .
-  FILTER NOT EXISTS { ?entity owl:deprecated true }
-  FILTER NOT EXISTS { ?entity2 owl:deprecated true }
-  FILTER (?entity != ?entity2)
+  ?entity ?property ?value .
   FILTER (!isBlank(?entity))
-  FILTER (!isBlank(?entity2))
+  FILTER NOT EXISTS { ?entity owl:deprecated true }
+  FILTER (UCASE(?value) = ?syn_std)
 }
-ORDER BY DESC(UCASE(str(?value)))
+ORDER BY DESC(UCASE(str(?value)))